Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

From Thermodynamics to Kinetics: Enhanced Sampling of Rare Events

(2015) Lijiang Yang et al.   ACCOUNTS OF CHEMICAL RESEARCH

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

(2015) Alejandro Gil-Ley et al.   Journal of Chemical Theory and Computation

Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations

(2015) Jun Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational Organic Chemistry: Bridging Theory and Experiment in Establishing the Mechanisms of Chemical Reactions

(2015) Gui-Juan Cheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface

(2014) Mingjun Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Stable Salt–Water Cluster Structures Reflect the Delicate Competition between Ion–Water and Water–Water Interactions

(2014) Cheng-Wen Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computer Simulation Studies of Aβ37–42 Aggregation Thermodynamics and Kinetics in Water and Salt Solution

(2014) Y. Isaac Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Pd(II)-Catalyzed meta-C–H Olefination, Arylation, and Acetoxylation of Indolines Using a U-Shaped Template

(2014) Guoqiang Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformation-induced remote meta-C–H activation of amines

(2014) Ri-Yuan Tang et al.   NATURE

Dynamics of spontaneous flipping of a mismatched base in DNA duplex

(2014) Y. Yin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meta-Selective C–H Functionalization Using a Nitrile-Based Directing Group and Cleavable Si-Tether

(2013) Sunggi Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cross-Coupling of Remote meta-C–H Bonds Directed by a U-Shaped Template

(2013) Li Wan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cis–Trans Isomerizations of Proline Residues Are Key to Bradykinin Conformations

(2013) Nicholas A. Pierson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synthesis, Structure, and Catalytic Studies of Palladium and Platinum Bis-Sulfoxide Complexes

(2013) Emma E. Drinkel et al.   ORGANOMETALLICS

Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-β

(2013) Fahimeh Baftizadeh et al.   PHYSICAL REVIEW LETTERS

Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail

(2012) Fahimeh Baftizadeh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Activation of remote meta-C–H bonds assisted by an end-on template

(2012) Dasheng Leow et al.   NATURE

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

(2012) Fan Jiang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation

(2011) Qiang Shao et al.   JOURNAL OF CHEMICAL PHYSICS

Number of Solution States of Bradykinin from Ion Mobility and Mass Spectrometry Measurements

(2011) Nicholas A. Pierson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Preparation, Structure, and Reactions of Trifluoroacetimidoyl Palladium(II) Complexes

(2011) Hideki Amii et al.   ORGANOMETALLICS

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Evidence for a Quasi-Equilibrium Distribution of States for Bradykinin [M + 3H]3+Ions in the Gas Phase

(2010) Nicholas A. Pierson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Novel Fluorinated Gold(I) N-Heterocyclic Carbene Complex: Exploiting Fluorine Stereoelectronic Effects To Control Molecular Topology

(2010) Susann Paul et al.   ORGANOMETALLICS

Study of bradykinin conformation in the presence of model membrane by Nuclear Magnetic Resonance and molecular modelling

(2009) Claudia Bonechi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

A selective integrated tempering method

(2009) Lijiang Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison between integrated and parallel tempering methods in enhanced sampling simulations

(2009) Lijiang Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS

An integrate-over-temperature approach for enhanced sampling

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS

Stepwise evolution of protein native structure with electrospray into the gas phase, 10-12 to 102 s

(2008) K. Breuker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding organofluorine chemistry. An introduction to the C–F bond

(2007) David O'Hagan   CHEMICAL SOCIETY REVIEWS